Sponge assemblages were investigated in the Spermonde Archipelago, southwestern Sulawesi, Indonesia. In this study spatial patterns of sponge similarity among sites were significantly related to remotely sensed environmental variables, the degree of human settlement and depth, but not to the distance between sites. Both oviparous and viviparous species groups responded to similar environmental constraints, and differences in similarity were unrelated to the distance between sites. The degree of human settlement, however, was significantly related to variation in the composition of viviparous, but not oviparous species. Our results demonstrate, most importantly, the utility of remotely sensed data in predicting the spatial turnover of diverse species assemblages such as sponges. Secondly, they show that patterns of human settlement in the Spermonde Archipelago appear to be affecting patterns of sponge beta diversity. These results highlight the need to assess and protect marine areas in biodiversity hotspots such as Indonesia.